Gene expression is the main driver of purifying selection in large penguin populations
Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species' lineages, pointing toward...
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ftccsdartic:oai:HAL:hal-04307140v1 2024-02-27T08:35:38+00:00 Gene expression is the main driver of purifying selection in large penguin populations Trucchi, Emiliano Massa, Piergiorgio Giannelli, Francesco Fernandes, Flavia, a N Ancona, Lorena Stenseth, Nils, Chr Obiol, Joan, Ferrer Paris, Josephine Bertorelle, Giorgio Le Bohec, Céline Institut Pluridisciplinaire Hubert Curien (IPHC) Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS) 2023-11-25 https://hal.science/hal-04307140 https://hal.science/hal-04307140/document https://hal.science/hal-04307140/file/Trucchi-Bioarxiv-2023.08.08.552445v1.full.pdf https://doi.org/10.1101/2023.08.08.552445 en eng HAL CCSD info:eu-repo/semantics/altIdentifier/doi/10.1101/2023.08.08.552445 hal-04307140 https://hal.science/hal-04307140 https://hal.science/hal-04307140/document https://hal.science/hal-04307140/file/Trucchi-Bioarxiv-2023.08.08.552445v1.full.pdf BIORXIV: 2023.08.08.552445 doi:10.1101/2023.08.08.552445 info:eu-repo/semantics/OpenAccess https://hal.science/hal-04307140 2023 Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes [SDV]Life Sciences [q-bio] info:eu-repo/semantics/preprint Preprints, Working Papers, . 2023 ftccsdartic https://doi.org/10.1101/2023.08.08.552445 2024-01-28T00:19:34Z Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species' lineages, pointing towards gene expression as an additional driver of purifying selection. However, estimates of the effect of gene expression on segregating deleterious variants in natural populations are lacking, as well as an understanding of the relative contribution of population size and gene expression to overall purifying selection pressure. Here, we analyse genomic and transcriptomic data from two natural populations of closely related sister species with different demographic histories, the Emperor (Aptenodytes forsteri) and the King penguins (A. patagonicus), and demonstrate that purifying selection at the population-level depends on the level of gene expression, with larger effects than population size. Deleterious segregating variants spread less in the population when they are in genes with higher expression rate. Leveraging realistic forward simulations, we estimate that the top 10% of the most highly expressed genes in a genome experience a selection pressure corresponding to an average selection coefficient of-0.1, which decreases to a selection coefficient of-0.01 for the top 50%. Gene expression appears to be a fundamental driver of purifying selection in natural populations, also effective at small population size. We suggest gene expression could be used as a proxy for gene selection coefficients (i.e., distribution of fitness effects), which are notoriously difficult to derive in non-model species under real-world conditions. Report Aptenodytes forsteri King Penguins Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes [SDV]Life Sciences [q-bio] |
spellingShingle |
Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes [SDV]Life Sciences [q-bio] Trucchi, Emiliano Massa, Piergiorgio Giannelli, Francesco Fernandes, Flavia, a N Ancona, Lorena Stenseth, Nils, Chr Obiol, Joan, Ferrer Paris, Josephine Bertorelle, Giorgio Le Bohec, Céline Gene expression is the main driver of purifying selection in large penguin populations |
topic_facet |
Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes Purifying selection E-R anticorrelation forward simulations non-model species Aptenodytes [SDV]Life Sciences [q-bio] |
description |
Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species' lineages, pointing towards gene expression as an additional driver of purifying selection. However, estimates of the effect of gene expression on segregating deleterious variants in natural populations are lacking, as well as an understanding of the relative contribution of population size and gene expression to overall purifying selection pressure. Here, we analyse genomic and transcriptomic data from two natural populations of closely related sister species with different demographic histories, the Emperor (Aptenodytes forsteri) and the King penguins (A. patagonicus), and demonstrate that purifying selection at the population-level depends on the level of gene expression, with larger effects than population size. Deleterious segregating variants spread less in the population when they are in genes with higher expression rate. Leveraging realistic forward simulations, we estimate that the top 10% of the most highly expressed genes in a genome experience a selection pressure corresponding to an average selection coefficient of-0.1, which decreases to a selection coefficient of-0.01 for the top 50%. Gene expression appears to be a fundamental driver of purifying selection in natural populations, also effective at small population size. We suggest gene expression could be used as a proxy for gene selection coefficients (i.e., distribution of fitness effects), which are notoriously difficult to derive in non-model species under real-world conditions. |
author2 |
Institut Pluridisciplinaire Hubert Curien (IPHC) Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS) |
format |
Report |
author |
Trucchi, Emiliano Massa, Piergiorgio Giannelli, Francesco Fernandes, Flavia, a N Ancona, Lorena Stenseth, Nils, Chr Obiol, Joan, Ferrer Paris, Josephine Bertorelle, Giorgio Le Bohec, Céline |
author_facet |
Trucchi, Emiliano Massa, Piergiorgio Giannelli, Francesco Fernandes, Flavia, a N Ancona, Lorena Stenseth, Nils, Chr Obiol, Joan, Ferrer Paris, Josephine Bertorelle, Giorgio Le Bohec, Céline |
author_sort |
Trucchi, Emiliano |
title |
Gene expression is the main driver of purifying selection in large penguin populations |
title_short |
Gene expression is the main driver of purifying selection in large penguin populations |
title_full |
Gene expression is the main driver of purifying selection in large penguin populations |
title_fullStr |
Gene expression is the main driver of purifying selection in large penguin populations |
title_full_unstemmed |
Gene expression is the main driver of purifying selection in large penguin populations |
title_sort |
gene expression is the main driver of purifying selection in large penguin populations |
publisher |
HAL CCSD |
publishDate |
2023 |
url |
https://hal.science/hal-04307140 https://hal.science/hal-04307140/document https://hal.science/hal-04307140/file/Trucchi-Bioarxiv-2023.08.08.552445v1.full.pdf https://doi.org/10.1101/2023.08.08.552445 |
genre |
Aptenodytes forsteri King Penguins |
genre_facet |
Aptenodytes forsteri King Penguins |
op_source |
https://hal.science/hal-04307140 2023 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1101/2023.08.08.552445 hal-04307140 https://hal.science/hal-04307140 https://hal.science/hal-04307140/document https://hal.science/hal-04307140/file/Trucchi-Bioarxiv-2023.08.08.552445v1.full.pdf BIORXIV: 2023.08.08.552445 doi:10.1101/2023.08.08.552445 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1101/2023.08.08.552445 |
_version_ |
1792042374510149632 |